Electrical – LPc11u68 Recognized as an USB mass storage device even when programmed in HID class

Lookup forebrain code examples, they use NXP LPC1343 chip that has USB mass storage drivers in ROM (so you can program the chip via drag and drop). Forebrain have example where they use internal ROM driver to present an EEPROM chip or simply just piece of RAM as mass storage device. They are closed source, but this gives the idea of how it could be implemented.

In general, you have to implement specific USB mass storage driver hooks.

There is no need to make config file in any special format as you could implement FAT system on your chip so it accesses flash memory as FAT filesystem. You can lookup any SD card reading/writing example for popular microcontrollers - some use low level, some implement FAT. Particulary - this one for LPC1343 implements FAT over SD card: https://github.com/Miceuz/LPC1343CodeBase/tree/master/drivers/fatfs

BTW, have you considered an option to put configuration into a file on SD card? You would have loads of ready made code and examples for broad range of MCUs for that. Config process would involve extracting SD card from device and putting it into computer though.

The USB Serial Number is what you want. And Atmel has a small datasheet on how to implement it with their usb stack here.

Additionally, any of the user configurable USB descriptors could be used. Assuming you are using the same VID/PID pair, you still have the Device Release Number, Manufacturer String Descriptor (Manufacturer Name), Product String Descriptor (Product name), and the Serial Number Descriptor, all of which go into the basic usb device descriptor that is mandatory for any usb device. They are independent of the usb class (HID, CDC, Proprietary etc), all major OS can read them, and can be as unique as you need them to be.